stevenysw / helminthr Goto Github PK

Programmatically access the London Natural History Museum's helminth database.

See software note in Ecography (available here)

# From GitHub
# install.packages("devtools")
devtools::install_github("rOpenSci/helminthR")
library("helminthR")

Given a host genus and (optionally) species and location, this function returns all host-parasite associations of a given host species. The example below determines all parasite records for helminth infections of Gorilla gorilla.

gorillaParasites <- findHost('Gorilla', 'gorilla')
head(gorillaParasites)

Given a helminth parasite genus (and optionally species, and location), this function returns a list of host-parasite records for that parasite. In the example below, I query the database for occurrences of the genus Strongyloides.

strongHosts <- findParasite(genus='Strongyloides')
str(strongHosts)

List all location names (listLocations()). These names can be given to the findLocation() function, which finds all host-parasite associations that have occurred in the given location. Below, I look at host-parasite associations recorded in France.

FrenchHostPars <- findLocation(location='France')
str(FrenchHostPars)

Feel free to fork it and contribute some functionality.